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Kennedy, the patriarch of one of the great Catholic political families of the 20th century, frequently sided with the Church on social justice issues such as labor rights, immigration, aid to the poor and health care. However, through much of his legislative career, Kennedy’s positions on issues such as abortion rights, same-sex marriage and embryonic stem cell research differed markedly from Church teachings.

Some Catholics, particularly pro-life activists, had contended that the cardinal should not have presided over the senator’s funeral, while others claimed that Kennedy should not have been allowed a public funeral Mass at all.

In his post, Cardinal O’Malley explained that he attended the liturgy out of respect for the senator and the Kennedy family, as well as a tribute to his accomplishments throughout his political career.

“The thousands of people who lined the roads as the late Senator’s motorcade traveled from Cape Cod to Boston and the throngs that crowded the Kennedy Library for two days during the lying in repose, I believe, were there to pay tribute to these many accomplishments rather than as an endorsement of the Senator’s voting record on abortion,” Cardinal O’Malley wrote in his Sept. 2 post on cardinalseansblog.org.

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Cardinal O’Malley also noted Kennedy’s letter to Pope Benedict, which President Obama personally delivered when he visited the Vatican in July. In the portion of the letter read at his internment at Arlington National Cemetery, the late senator acknowledged that he was not always a faithful Catholic, asked for prayers near the end of his life, and pledged to pray for the Church. In his response, the Holy Father commended the Kennedys to the intercession of the Blessed Mother and imparted his Apostolic Blessing.

“As Archbishop of Boston, I considered it appropriate to represent the Church at this liturgy out of respect for the Senator, his family, those who attended the Mass and all those who were praying for the Senator and his family at this difficult time,” Cardinal O’Malley wrote. “We are a people of faith and we believe in a loving and forgiving God from whom we seek mercy.”

C.J. Doyle, executive director of the Catholic Action League of Massachusetts called the funeral Mass “a tragic example of the Church’s willingness to surrender to the culture, and serve Caesar rather than Christ.”

“No rational person can reasonably be expected to take seriously Catholic opposition to abortion when a champion of the Culture of Death, who repeatedly betrayed the Faith of his baptism, is lauded and extolled by priests and prelates in a Marian basilica,” said Doyle.

Father Martin added that Cardinal O’Malley’s presence puts the Church “in the best possible light.”

“Cardinal O’Malley has been clear about his strong opposition to abortion and same-sex marriage,; his simple presence at the funeral shows his support of forgiveness, compassion, and that quality that is perhaps most missing in today’s church: mercy,” he said.

In his blog post, the cardinal’s also offered details on his brief conversation with President Obama following the Mass. According to the post, the cardinal welcomed the president to the basilica and affirmed the American bishops’ support of universal health care. However, the cardinal also told President Obama that the U.S. bishops will not support a plan that provides for abortions.